Evangelion: Nemesis
by 38th Parallel
Summary: Shinji is absorbed by Unit 01 during his first battle with the angels. What he encounters while absorbed, changes his life forever.
1. Prologue: Preparation

DISCLAIMER: I don't own Neon Genesis Evangelion or any of the characters associated with the series. GAINAX owns the rights to this series.

A/N - First and foremost, I would like to inform you that Shinji is very OCC in this story. If you are a fan of the shy and introverted Shinji, you have been warned. Also, the events of this story take place after Episode 1 in which Shinji loses consciousness during his first battle with the angels. Some things might not necessarily make sense in comparison to the actual story because it deviates quite a bit due to the nature of the plot, but this is my first attempt at this, so please bear with me!

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Prologue - Preparation

It's never an easy thing to wake up with a severe headache.

This was no exception for young Shinji Ikari as he opened his eyes to find an unfamiliar ceiling. Just yesterday, he had felt uncertain, depressed, unwanted...

Now, he was different. He actually thanked his father for giving him this opportunity. Forcing him to pilot the EVA and risk his life against the angel had changed his life forever...

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_"Do you understand what you have to do, Shinji?" asked Yui Ikari for the third time._

_"Yes mom, I do." Shinji replied. _

_So this was what having a parent was like. They liked to tell you what you already knew and repeat themselves unnecessarily seemingly just to annoy you._

_It felt good._

_It felt good to know that someone cared enough to repeat things to the point of annoyance just to make sure you understood. It felt good to have someone that constantly reminded you that they were on your side no matter what. _

_It felt good...just for once, not to feel used..._

_It was almost time. In this vaccuum inside the consciousness of EVA, months had passed. Five glorious months while in the outside world, only a few hours had passed. During this time of euphoria, Shinji had been reunited with the consciousness of his mother, who had taken physical form inside Evangelion Unit 01. His mother had then taught him all that she knew about Project EVA, his father, NERV, and most importantly, SEELE. Some of the things he had learned had mortified him, and some of it shook him still. Most of what he was told would have been too much for a normal 14 year old boy to take in. However, Shinji was stronger in heart than most 14 year olds and, although he didn't know it, Yui Ikari did. As his mother, she knew Shinji more than anyone else alive. She knew he was capable of correcting the chain of disastrous ambitions that she had so foolishly helped ignite. So, in order to correct her mistakes and give Shinji a fighting chance at a normal future, Yui had given him a gift both terrible and invaluable. Knowledge. She knew this was a terrible thing to ask of him and it tore her apart inside. However, both Shinji and Yui knew that in order for humankind, including Shinji, to survive, Shinji had to endure suffering a little longer. _

_But at the same time, Yui had given Shinji love. Unconditional love that he had so desired for all of his life but had never received. It had torn her apart when she had first laid her eyes on him staring back at the giant monstrosity that was EVA. His eyes had been so full of pain, crying out for years of loneliness and misery. Then, a slight glimmer of hope had appeared in those beautiful eyes when he saw his father, Gendo. 'Maybe things would be different,' she could almost hear him hope, 'maybe he wanted me back as a son...' And those hopes only to be crushed by Gendo's selfishness and cruelty. The last flicker of hope that Shinji had the capacity to carry had disappeared with that, and Yui Ikari knew she had to do something to help her son._

_So she had. During Shinji's first battle with the angels, Yui had caused the EVA to go berserk and absorb Shinji into itself, causing his body and soul to maintain a physical form within the consciousness of the EVA. Now Shinji was ready to go back to the world. Although it pained her greatly to see him go, Yui was content just to have been able to let him know that she will always be with him. That any battle he fights, will be with her. That he will never be alone._

_It was time. _

_Shinji hugged his mother one last time, tears freely rolling down his face. "You're a grown man now Shinji." said Yui, fighting to keep her voice steady. "Go out there and make me proud."_

_"I will." Shinji replied, determination shining in his eyes as the pain of farewell reflected across them. "I'll make you proud mother."_

_Yui smiled. "You already have, more than you could know. I love you Shinji, remember that. And whatever you do, despite all the things you have to do, don't let yourself turn into someone like your father. You must be able to control your emotions, not banish them forever."_

_"Don't worry. I'll find a hot girlfriend and introduce you to her just to prove I'm not an emotionless robot." Shinji said, half a smile on his face._

_Yui laughed. "You do that! I'll hold you to it."_

_Then, with a final hug and a final memory of each other's smiling faces, Shinji drifted off into unconsciousness as Yui sent him back to the outside world._

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[PA System] "Captain Misato Katsuragi and Doctor Ritsuko Akagi please report to Room 2A. Captain Katusragi and Doctor Akagi you are needed in Room 2A please."

Shinji looked up at the security camera monitoring him from his bed and smiled sadly.

_Here we go_.


	2. Chapter 1: Foundations

DISCLAIMER: I don't own Neon Genesis Evangelion or any of the characters associated with the series. GAINAX owns the rights to this series.

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Chapter 01 - Foundations

"Welcome to your new home!" Misato exclaimed cheerfully, welcoming Shinji into her apartment. He had thought he would be able to find his own place to live but unfortunately, he had no idea where to even start. Also, there was the fact that he was seriously underage. It was just as well. Misato seemed like a nice person and she had spent most of the time Shinji was at the hospital with him, just to make sure he was ok. Shinji stepped through the threshold in anticipation.

The place was a mess! Empty beer cans everywhere, packages of half-eaten TV dinners littering the counters and spilling over into the living room, and piles of dirty laundry strewn about the entirety of the apartment were just some of the things that Shinji noticed as soon as he entered Misato's apartment. Just with that quick scan of the apartment, Shinji could already tell that living with this woman was not going to be easy.

A lot of work would have to be done in order to turn this place from the pig stye that it was into an actual human inhabitance, but Shinji didn't mind too much. He was used to doing household chores from when he used to live with his teacher. Although this was exponentially worse, it was basically the same concept. Once the trash was thrown out, 90% of the cleaning would be done. Shinji briefly even considered throwing Misato out with all the trash. Briefly.

"Great!" replied Shinji, trying to sound as optimistic as possible. "Thanks for taking me in. I really appreciate it."

"No worries, it's not like we could let a 14 year old live by himself! Would you like something to drink?" Misato asked as she opened the fridge, "we have...um. Beer." Misato peered around at Shinji with a peevish grin. "I guess we're going to have to do some shopping. Can't really feed you beer right?"

Shinji chuckled. "It's just as well. I need to pick up a few things before school starts anyways. So which one is my room? And do you drink _anything_ besides beer?" asked Shinji as he looked incredulously around at the thousands of beer cans littered across the hallway.

Laughing , Misato led Shinji through the kitchen and into the living room, she pointed to the room on the right down the hall. "It should be empty, go ahead and put your things down and make yourself comfortable. I'll order some in some Chinese for dinner. And I try to keep to a very consistent diet of beer and take out."

Shaking his head disbelievingly, Shinji made his way towards his new room. "Wow. Anyways, Chinese sounds good, thanks!" called out Shinji as he opened the door to the room. It was a modestly sized room but he didn't mind at all. Amazingly enough, this seemed to be the only part of the apartment that did not have garbage littered about the entire room and he was actually quite content with just that fact. Opening up his duffel bag, Shinji unpacked his belongings, which consisted of 3 white shirts, 2 black slacks, a few pairs of socks and underwear, a laptop, and a SDAT player. Pausing, Shinji took a moment to contemplate the SDAT player lying on his new bed. After a moment, with a determined expression on his face, Shinji took the player and threw it in the trash bin next to his new desk.

It was the start of a new life.

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The next morning, Misato took Shinji with her to NERV headquarters for the first day of training. As they made their way down to Central Dogma, Misato noticed Shinji wringing his hands nervously.

"You ok Shinji?" Misato asked.

"Yeah, just a little bit nervous I guess. I'll be fine, thanks." replied Shinji.

"Don't worry. I'm sure you'll be fine."

As the elevator made its way further down into Nerv HQ, Shinji contemplated what he would be faced with once he started his training. The truth was, he had no idea what to expect once he got back into the cockpit of his EVA. Will he be able to sense his mother again? Will he even be able to move his EVA? It seemed a likely possibility that he would just be back to square one and have to go through the learning process all over again starting from learning how to walk with the EVA. He was aware of the general theory behind EVA piloting, as his mother so kindly spent hours and hours teaching him, but theoretical knowledge was just that, theoretical. Unpracticed. For all he knew, the first time he piloted the EVA against that angel could have just been a fluke. Maybe he wouldn't even be able to move it this time. No, his mother was there. He had to believe that she would guide him through. Shaking off the feeling of uncertainty, Shinji steeled himself as the elevator reached floor B20.

"Ok Shinji, I will be down at the Command Center. Ritsuko here will look after you from here on." said Misato as she got off with Shinji close behind. Winking, Mistao added loud enough to hear, "Oh, and try not to goggle too much at her like you did with me. Remember, our eyes are up here!"

Laughing at the horrified expression on Shinji's face, Misato walked off towards her office.

Shinji whipped around to face Ritsuko, beet red and trying to make it as plain as possible that his eyes were focused on her face. "I never- I mean, I don't thin-" spluttered Shinji, trying to defend himself. What was that woman thinking? He had never done such a thing! It was true that she was very attractive, especially for a woman so much older than he was, but there was never an incident even close to what she had just planted in Ritsuko's head!

Ritsuko laughed. "Don't worry Shinji, I'm sure you are a perfect gentleman." said Ritsuko seemingly unconcerned about what Misato had just said. "So how are you today?"

Barely holding in a sigh of relief, Shinji followed after Ritsuko as she led the way toward the command center where her office was located. "I'm ok, considering" replied Shinji, recovering from the initial shock. "It's not every day you get to save the world while knocked unconscious, is it?"

Ritsuko stopped and turned to face Shinji with a wondering look on her face. "I must have misjudged you Shinji. When I first met you, I figured you would be pretty shy and introverted. I guess it's true what they say. You can't judge a book by its cover."

Shinji shrugged. "I figured, since I will be working with all of you, might as well be social. Will you be conducting my training then ma'am?"

"Misato and I will both be conducting your training. Misato will, of course, train you in combat and tactics as you pilot your EVA while I will make sure your physical condition as well as your mental connection with the EVA remains stable." explained Ritsuko as she led Shinji to her office. "We're going to start off with a few tests in my office and then we'll go ahead and see how you do in the plug."

"Whatever you say, ma'am."

Ritsuko smiled. "Oh, and feel free to call me Ritsuko! Like you said, we'll be working together so I want you to feel comfortable with me."

Shinji smiled back. "I'll try thanks. And I swear I never stared."

Chuckling, Ritsuko replied, "I believe you Shinji. Relax."

Two hours of testing later, after which Shinji was entirely convinced that he would _never_ be comfortable with Ritsuko, Shinji was given a plug suit to change into and led to EVA Unit 01.

Walking down to the EVA Hangar, Shinji looked up at the giant purple mecha. This was the first time he saw the EVA after he had been released from the hospital. A surge of emotions threatened to overwhelm him as he unconsciously reminded himself that his mother's soul was within that disgusting looking bioweapon. Fighting down the urge to throw up, Shinji forced himself up to the Entry Plug with the help of a few technicians who were preparing the EVA for testing.

Climbing into the cockpit, Shinji looked around in nostalgia as he recalled the day of his first fight with an angel. He could still recall the splitting pain in his head from when the angel had crushed the head of the EVA. Remembering the pain, he also remembered that it hadn't been so long ago. Shuddering, Shinji took his place within the cockpit and put on is A-10 Neuron Transmitters. As he did so, Shinji heard Misato's voice through the comlink system. "Hey Shinji, I heard you had a pretty tough time in there. You alright?"

"Are you kidding me? I never want to be tested like that again. I felt like a gorilla at a zoo." groaned Shinji. "I think I'm already starting to hate Dr. Akagi."

Misato chuckled. "Oh, by the way, you're on the global comlink Shinji, everyone can hear you."

"...Oh."

"Don't worry Shinji. I understand you would feel that way after all that man-handling." chuckled Ritsuko over the comlink. "Let's start the test shall we?"

"Sure. Better now than later." said Shinji, starting to become nervous.

"Commencing Synchronization."

"Inserting Entry Plug"

"Direct hydro-transmission system, connetion prepared."

"Plug fixed in place."

"First stage connection initiated."

"Filling the entry plug."

"Connecting main power."

"Commencing secondary contacts. A-10 nerve connection, normal."

"Thought configuration, Japanese. All preliminary contacts established."

As Shinji breathed in the LCL, he went through all the things his mother had taught him about the EVA. This was the first step. He had to make sure he had this right. Focusing his mind, Shinji mentally reached out towards the EVA, towards the soul of his mother he knew existed within.

A few moments later, he knew he had it. He felt his mother's embrace course through him as he connected to the soul of his mother and, by extension, the EVA. As he opened his eyes, which he had not even realized he had squeezed shut for concentration, he felt the eyes of the EVA lighting to life bring images of the hangar into view.

"Bi-directional circuits are open. Synchronization rate-oh my god!!! Synchronization rate steady at 81.3%!!!"

"What?! Impossible!!" Ritsuko exclaimed. Shinji could see her and Misato rushing over to Maya Ibuki's station to verify what they had just heard. In fact, the entire bridge had crowded around Maya's station in disbelief.

However, in the midst of all this chaos, Shinji's eyes were only on one person. As he looked through his EVA to the man sitting atop the command center, Shinji thought he saw the man's fists shaking.

He had succeeded. He had taken the first step, and with that came a feeling of confidence such as he had never felt before.

Shinji smiled.

_Thank you mother._

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Please Read and Review! Hope you liked the first chapter. More to come soon!


	3. Chapter 2: Integration

DISCLAIMER: I don't own Neon Genesis Evangelion or any of the characters associated with the series. GAINAX owns the rights to this series.

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Chapter 02 - Integration

"Shinji this is amazing!" Ritsuko exclaimed over the comlink. "It's unprecedented. We were pretty shocked a few days ago during your first synchronization with Unit 01, but this! Amazing. Just. Amazing!"

The command bridge was bustling with activity as technicians ran back and forth, comparing data and discussing possibilities. Everybody appeared excited. Just a few days ago, these technicians seemed on the verge of a nervous breakdown because they couldn't be sure if Shinji would be able to pilot the EVA so that he could face the invading monstrosity. Now, they looked at Shinji as if he would be the savior of them all. Shinji Ikari, the prodigy who had achieved a stable 81.3% sync rate on his first day of training. This was along the lines of what everyone observing the synchronization testing was thinking, except, of course, for a select few sitting at the highest point of the command bridge. That is, this was what they were thinking until Shinji was put into a simulation program for target practice.

"Shinji! You just point and shoot! Just point. And shoot! It's _not that hard_" Misato yelled for the fifth time, clearly frustrated beyond belief. The problem wasn't with Shinji's ability to control the EVA. He could move just fine with the simulated EVA. It was responding to his every thought with a negligible margin of delay. If they asked him to somersault over a building or do a cartwheel on the simulated streets of Tokyo-3, he could have done so with no problems. But he had never handled a gun before in his life, of course he had no idea how to shoot it! It was easy for Misato to say since she had gone through proper training with guns as a military officer. Shinji, on the other half, was just a fourteen year old boy.

Shinji winced as the angel tackled him yet again and sent his EVA crashing into a nearby office complex. Yet again, the simulation ended with Shinji having been defeated by the EVA. "Let's call it a day Misato" said Ritsuko. "I think the poor boy's been through enough-"

"I'm fine ma'am. I can continue." cut in Shinji. "I can't leave it like this right? What if an angel attacks tomorrow? Or even tonight? I would prefer not to be put into a situation like the last time, totally unprepared."

"Good. I admire your persistence." chimed in Misato. She was beginning to find more and more respect for the boy. It was almost as if she had never seen him break down that first day before he was forcefully put into the pilot seat of Unit 01. But then, who wouldn't break down in a situation like that? "Alright, let's try again!"

Shrugging, Ritsuko rebooted the simulation program and configured it to EVA Unit 01. As she did so, she risked a glance up at the Commander of NERV, who had been watching the entire training process. He did not look too happy. Gendo Iarki rarely did, when things were not going according to his plans. This new development with Shinji definitely presented a problem. Gendo knew that only Shinji could pilot the EVA so he could not replace him. At the same time, Shinji's new-found...confidence might pose a problem in the future. His son would have been much easier to manipulate as an insecure, unstable boy rather than...this. As the simulation started back up, Gendo stood up and turned to Sub-Commander Kozo Fuyutsuki. "Watch over the rest of this and report anything I might need to know, professor." Without waiting for the Sub-Commander's nod of understanding, Gendo strode out of the bridge room. He had a lot of thinking to do.

Shinji was now back in the simulation.

_Point and Shoot. Point and Shoot. Why the hell is it so hard to point and shoot?!_

The simulation always started the same way. A reconstruction of the battle against the third angel, Sachiel. Of course, Shinji had lost consciousness almost at the beginning of that battle, but he remembered what the angel had looked like and it still brought shudders up and down his spine thinking about it.

There it was. Shinji hid behind a tall skyscraper and carefully listened as the angel advanced further into the city towards the Geofront. He took a second to check that his standard issue EVA Pallet Gun was loaded and ready, and went back to scanning the area for any possible surprises.

"Distance to target, 800 meters." announced Misato. "wait for my mark."

"700 meters...600 meters...remember Shinji, you are aiming for its core, not the buildings to either side of it..."

"Wow. Thank you, I had no idea." grumbled Shinji.

"GO!"

Shinji ran out from the cover of the building, firing in bursts at, what he hoped, was the angel's core.

He missed.

_Shit!_

Shinji dove to the ground and rolled on to his knees as the angel's arm lance shot past where his head had been just a second ago. Stabilizing his aim, Shinji aimed and shot again. Miss. The angel was approaching rapidly. He could hear Misato yelling in the background but he was too caught up in the adrenaline rush to make out what she was saying. The angel was fast approaching, about 200 meters away now. He kept up the hit and run tactic, diving out of the way as Sachiel`s arm lances continued their assault.

Only 100 meters away now. Cursing, Shinji unloaded the rest of his magazine on a nearby building, causing it to crumble in front of the angel. Using the dust caused by the debris to buy him some time, Shinji tossed his gun away and took out his prog knife. He couldn`t understand why he couldn't hit the target. He was aiming straight at the damn thing and firing but it seemed to consistently miss. Dismissing those concerns for later, Shinji ducked behind a medium sized office complex and crept around the block to flank the angel.

Unfortunately, the angel seemed to realize what he was doing and fired a beam of laser from his eyes, destroying the building he was taking cover under.

_Oh, to hell with this!_

Cursing yet again, Shinji charged. Another beam of laser just missed him as he dove to the ground, rolled, and was charging again in one fluid motion. Shinji could feel sweat coming out of his pores and dissolving into the LCL as his heart pounded in his ears. Dodging the lances left and right, rolling out of the way of laser beams, Shinji felt like it had been hours before he was almost within reach of the angel. But then he was there, and squatting down to avoid another attack, Shinji sprang forward propelled by the mechanical muscles of the EVA and tackled Sachiel into the ground, burying his prog knife deep within its core as he did so. For a few seconds, Sachiel flailed, strugging to throw the EVA off its body, but then it was still.

He had succeeded. Not quite in the way they had hoped, but Sachiel was down for the count. Shinji finally focused back on the communication system, waiting to be scolded for ignoring orders, but no sound came from the comlink. Frowning, he turned on his visual monitors to see what was going on on the bridge.

The command bridge, once again, was staring collectively at the holographic projector with incredulous looks on their faces, completely dumbfounded. After a few moments, Misato recovered from the initial shock. "Shinji, that was amazing! I mean, you missed. It might have been much easier if you had just shot the damn thing, but your movements were spectacular! I had no idea the EVA could even move that fast!"

Needless to say, Shinji was more than slightly confused. He had thought that he would have gotten a lecture on the importance of obeying orders during combat and gibes about how he couldn't hit a target if it cost him his life, but...praise? He honestly hadn't planned on doing any of that; he had just been incredibly frustrated with his poor marksmanship and had just wanted to kill the damn thing for once. Thinking back on what he had just done, he couldn't really even understand what was so amazing about it. The angel had almost hacked him to pieces hundreds of times during those few minutes and he had barely escaped with his life. Well, hypothetical life, anyways. Deciding to ask Misato about it later, Shinji modestly dismissed the compliments, saying it had been chance, that he had had no idea what he had been doing, and if it would be ok to run the simulation again to improve his marksmanship.

A few hours later, at about 1 AM, Shinji and Misato collapsed on the couch in their living room, exhausted but content with the progress they had made that day. Shinji had finally been able to hit Sachiel at 500 meters dead on at its core and he had repeated the feat 3 times just to be sure he could do it. Even Ritsuko, a workaholic herself, had been amazed at Shinji's persistence and dedication to piloting. In truth, Shinji had enjoyed the experience. He relished the time he could stay connected to the EVA because he knew his mother was there, in essence, watching him and guiding him.

Misato lazily turned her head to face Shinji. "You were great today, Shinj. Just full of surprises, aren't you?" Shinji chuckled. "I try. So do I get a reward for all this hard work?" A mischievous glint appeared in Misato's eyes and Shinji quickly interjected, "I mean, I was wondering if you could maybe introduce me to the staff, maybe invite them over or something. I want to get to know them better." The glint had not disappeared from Misato's eyes, which worried Shinji. "Did you have someone in mind?" Misato asked, a slight hint of more teasing to come inflected in her tone of voice.

At being asked, an image of Maya Ibuko, one of the head computer technicians at the command center popped into Shinji's mind. Maya had shyly approached Shinji after his training session to welcome him to the team and to compliment him on the excellent work he had done today. She had been stuttering with her face crimson the entire time during the exchange, which had only really taken an upwards of 30 seconds as Shinji thanked her and excused himself to go get changed out of his plug suit. Shinji had figured that she was just naturally timid and dismissed her demeanor, but she had left a small impression on his mind. He thought she had a very nice smile, one full of sincerity and devoid of any personal intent. He could tell she smiled just because she wanted to smile. Dismissing Maya from his mind, Shinji replied. "Not really."

Misato inched closer. "Really? No one?" she asked suggestively. Sighing, Shinji pushed her away. "If I did, I would be crazy to tell you, wouldn't I?" replied Shinji. "Anyways, I'm headed to bed. Night Misato!"

Misato chuckled as she got up as well and headed towards her room. "Night Shinji, don't forget you have to be at school by 8 tomorrow! Don't want to be late on your first day right?"

Too tired to speak, Shinji waved a hand in acknowledgment and entered his room, falling asleep as soon as he hit the bed.

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The next morning, Shinji woke up to the sound of his alarm clock. Half-asleep, he made his way into the kitchen to grab a glass of water, then got washed up and ready for school. He could hear Misato snoring in her room indicating she was still asleep. 

_Lucky her._

Shinji walked out the door with a silent good-bye and headed to the school for his first day. It was actually a beautiful day outside. The sun was out, warming the air to a pleasant temperature with a slight breeze that kept the weather from being too hot. All in all, it felt like it would be a good day.

As he approached the school, he noticed two agents dressed in black suits standing at attention on either side of the entrance to the school. They seemed to be keeping an eye on Shinji and scanning everywhere for possible signs of trouble at the same time. As he passed by, they nodded in to Shinji in unison, which he returned. Unfortunately, what Shinji hadn't realized was that they never so much as blinked let alone acknowledge someone's presence. The fact that the two agents had gone so far as to _greet_ Shinji caused an uproar.

As soon as he stepped into the school grounds, a crowd of students charged him, bombarding him with questions and demands for information. "Woah! Are you an EVA pilot?" "Are those men here because of you?" "Are you like the son of the president?" "Do you know Rei Ayanami? She's another pilot!" "Can I get your autograph?" "What's your name?"

"Uh..." Shinji stammered, eyes widening at the sudden onslaught of attention. He had no idea how to act towards crowds like this, coming from the country where there were scarcely five people together.

"Alright! Alright! Break it up you guys! Let him have some room!" came a voice from outside the crowd. "Move out of the way!" The crowd parted to make room for a slender girl with freckles and dark brown hair. "Hi there!" she cheerfully greeted when she made it to where Shinji was standing. "I'm Hikari Horaki. I'm the Class Representative for class 2-A, I was told you were coming today so I came to show you around."

Breathing a sigh of relief, Shinji nodded and let Hikari lead him away from the crowd of students and into the school. "Nice to meet you Hikari. Wow, thanks a lot back there."

"Oh no worries. Most of the students here are sons and daughters of NERV employees so they get pretty excited when a new face shows up." explained Hikari. "Don't worry about it though, it will die down once they realize you're not a pilot."

"...right."

Hikari let Shinji to the second floor of the school building to classroom 2-A, instructing him to sit down at one of the desks towards the back of the classroom. As she was explaining the school regulations and class schedules for the semester, Shinji noticed Rei Ayanami staring out the window at the far side of the classroom.

Rei Ayanami.

Mother's clone.

He remembered when he had first seen her in front of EVA Unit 01. He had thought she was beautiful despite her horrific injuries. She had looked so fragile and he had instantly been overcome with a desire to protect her. Even now, for some reason, that desire remained in him. Shinji knew he should be disgusted by the very idea of a clone created with his mother's genes in order to act as a vessel for an angel, but he couldn't help but feel sympathetic towards her. She was, to him, just another victim of Gendo Ikari's cruel and selfish agenda.

"Shinji?"

Blinking, Shinji forced himself out of his thoughts. "Sorry Hikari, I was distracted. What'd you say?"

Hikari sighed. "Just remember to stop by the office after class to talk to the principal, ok?"

"Yeah, sure. Thanks." replied Shinji, having no clue what she had been talking about. Why did he need to go to the principal's office?

_Maybe it's something NERV related_.

Deciding to worry about that later, Shinji got to work in configuring his new school laptop for personal use. Not long after, students filled the class one by one, most of them giving Shinji a curious look before taking their seats. A few more minutes later, the teacher came in and the class bowed at Hikari's direction, indicating the start of class.

No sooner had classes started, a message popped up on Shinji's screen.

'Are you the pilot of the robot? Y/N'

Curious, Shinji tried to track the source of the message, hacking into the mainframe to try to locate the IP address of the sender. This was another thing he had learned while inside the EVA. His mother had taught him how to retrieve information from behind most security firewalls, so of course, the school security system was nothing to Shinji. Suddenly, another entity started creating additional defenses in the network to try to conceal his identity. Smiling, Shinji looked around the class to see who it could be. Closer to the front of the class, he saw a skinny brown haired boy typing furiously on his laptop. Then, realizing that he had been spotted, the boy turned around and shrugged, chuckling nervously. Then, another message popped up on his screen.

'You are, aren't you?'

Shinji gave up and decided to play along.

'Yes.'

All of a sudden, everyone in the class got out of their seats and crowded around Shinji, much to his surprise. "So you are the pilot! Wow!" "What's it like?" "How were you selected?" "What does the cockpit look like?" "Were you scared?"

"Uhh...I'm actually not allowed to talk about it...it's classified." replied Shinji, trying to ward off the questions. He could hear Hikari in the background trying to get everyone seated again, but amazingly enough, the teacher had noticed nothing and was continuously droning on about the political and economic affects of Second Impact. Then, the bell rang signaling the end of school.

Shinji quickly escaped the crowd muttering some excused about having to stop by the principal's office. Once there, Shinji was relieved to find that all the principal wanted was to welcome him to the school and let him know that Shinji's "situation" was completely understandable. Having gotten that over with, Shinji made his way out of the school to head home. Just outside though, a student in training pants and jacket approached him. "Ya Shinji Ikari?" he asked.

"Uh, yes. Who are you?"

"Toji Suzuhara, I'm in your class. Can you follow me for a second?"

Slightly confused but too curious to refuse, Shinji followed Toji around to the back of the school. The freckled boy from earlier was waiting there with giving Shinji a sympathetic look. Starting to feel suspicious, Shinji turned to Toji to tell him he was going to leave when, all of a sudden, he was looking up at the sky. For some reason, he was down on the ground with a very sore cheek. As he was still trying to figure out what had happened, he heard Toji say "Sorry transferee. But I have to hit you. I wouldn't have been satisfied unless I did."

_...what the hell?_

The other boy, named Kensuke, explained, looking down at him. "Sorry, but his younger sister got hurt in the battle. That's the reason."

Incredulous, Shinji got to his feet and stared at the bastard who was stalking off. "That's it? You come lead me out here and punch me while I wasn't looking like a bitch and then just run away?"

Of course, that brought Toji back. He looked furious.

Coming up to stand right in front of Shinji, he said. "Then watch this one very closely, punk." Shinji actually did see this one coming. Just as it was about to make contact with his face, Shinji caught Toji's fist with his left hand and threw his right fist into the other boy's face. This time, it was Toji`s turn to fall.

Kensuke, who had been watching the whole thing, was gaping at Shinji, flabbergasted at what just happened. Toji hadn't fared much better. In fact, he looked like he was wondering what had just happened as well. Then, Shinji saw Rei as she walked into view around the building.

"An emergency call..." said Rei. "I'll go first..."

Needing no further explanation, Shinji nodded as Rei ran off and turned to Toji, who was still trying to get back up. "What's her name?" Shinji asked.

"Mari."

Shinji nodded. "Tell her I'm sorry." said Shinji, genuinely meaning it.

With that, Shinji ran off towards NERV Headquarters.

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AN - Sorry this chapter was so boring! Just needed to lay in some groundwork. Oh and I apologize if there were any grammar/spelling mistakes. Still trying to find a proofreader. Read and Review please!


	4. Chapter 3: Combat

DISCLAIMER: I don't own Neon Genesis Evangelion or any of the characters associated with the series. GAINAX owns the rights to this series.

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Chapter 03 - Combat

"Target approaching at rapid speeds!"

"JSSDF VTOLS have engaged the target! ...target seems unaffected!"

"Captain Katsuragi! We just got a call from the UN ordering us to mobilize the Evangelions!"

Misato scoffed. "Idiots. Wasting tax dollars when they could have just sent us out from the beginning." Activating the comlink, Misato said, "Shinji! You are go for launch. You ok in there?"

"Ready."

"Start launch sequence!" commanded Misato.

Truth be told, she was more than a bit worried. Shinji had had only a day of training and she feared it might not be enough. Added to that, he had just undergone his first day at school. That should have been stressful for anyone, let alone someone who had the weight of the world on his shoulders.

Misato had only known Shinji for a short amount of time, but she had tremendous respect and admiration for him. A fourteen year old charged with serving as the last frontier for mankind. As the last line of defense. Even with that huge burden upon his shoulders, Shinji still had to endure the regular stresses and insecurities of a growing teenager. However, what was amazing was that Shinji acted as though he didn't mind at all. On the contrary, he was always cheerful and very approachable to anyone. Misato already knew for a fact that most of the crew on the command bridge regarded Shinji with the utmost respect, even after just one day of training and despite his young age. Not to mention a certain computer technician, who seemed to have a little crush on the boy. Shaking her doubts and musings out of her head, Misato concentrated on the task in front of her. Keep Shinji alive. As NERV's Tactical Operations Commander, she had the duty of making sure she did everything possible short of piloting the EVA herself to guarantee the safety of the pilot and the defeat of the target. If she could, she would rather be out there piloting the EVA and putting her life on the line rather than have to force Shinji to. But she couldn't. So instead, she would protect Shinji to the best of her abilities in the best way she could.

"The course is clear. All green. Evangelion Unit 01 is ready for launch."

Misato steeled herself. "Shinji, you ready for this?"

Shinji opened up a video link and gave Misato a wink, smiling, "Let's give it hell, captain."

Misato spared Shinji an encouraging smile before focusing her attention back on the holograph.

"Evangelion Unit 01. Launch!"

---

Toji watched Kensuke as his friend fidgeted with the video camera that he always carried around with him. Everyone had been hurried down to the underground shelters when the emergency alarm had sounded. He could see most of his classmates sitting nearby, talking and laughing as if there weren't anything going on above. Toji wasn't stupid. He knew the new kid - he was pretty sure Shinji was his name - had to put his life on the line to protect the city, and possibly the world. He also knew he probably deserved the punch he got from Shinji, because without the EVA pilot, his sister, not to mention himself, would probably be dead or worse at this point. But he didn't regret the exchange of blows. He had felt the need to do it, and he had done it. That was all it was.

"Hey Toji" whispered Kensuke, who had finished playing with the settings on his video camera. "I gotta talk to you for a sec." When Toji nodded, Kensuke dragged him over to the class rep, HIkari Horaki. As the class representative, Hikari was in charge of keeping the students of class 2-A organized although Toji thought she took the responsibility way too serious. Still, she had a pretty nice body and a cute face - when she wasn't yelling at "Suzuhara" not to be stupid, that is.

"Hey Class rep," Kensuke said, getting her attention. "We gotta use the bathroom real quick."

"Now? You guys should have gone hours ago!"

"I know, sorry class rep. But when ya gotta go, ya gotta go. Ya know?" replied Kensuke with an apologetic grin on his face.

Hikari sighed. "Alright, but make it quick ok?" she said, with what seemed to be a worried glance over at Toji.

_She probably thinks I'm going off to make more trouble._

"Sure thing!" replied Kensuke dragging Toji off to where the bathrooms were. Once he was sure no one was listening, Kensuke rounded on Toji with a wide grin on his face. "Dude, we gotta go up there man."

"Up where?"

"Up to the surface! I bet there's a huge battle up there right now! I gotta see this!"

""Are you crazy?" shouted Toji. "We'll get killed up there! Didn't you see what happened to Mari?!"

"I know, but even if I die, I want to see the thing just once! Come on!" begged Kensuke. "We can look after each others' backs and if you think it's too dangerous once we're up there, we'll come straight back down!"

Toji sighed, resigned. This was going to be a very, very bad idea...

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"Alright Shinji, we're just going to start off with a bit of reconnaissance. We just want to see what this thing can do, so keep your distance." ordered Misato.

"Roger that."

The angel looked like a giant...bug. There was no other way to describe it, really. It looked like a giant bug with tentacles. And harmful bugs had to be crushed. Shinji fired a burst at the angel, aimed directly at its core, but about 50 meters away from the target, the bullets hit an invisible barrier and dropped away, useless.

"Misato, the angel has an AT Field up!"

"I see it too Shinji, keep your distance for now!"

So Shinji kept his distance. Or tried to. The long tentacles of what seemed like energy beams kept dashing out at Shinji, trying to slice him open like it had done with all the buildings around them. Not only that, the thing was fast! Every second it seemed to be gaining on Shinji as it pursued the EVA. Cursing, Shinji continued dodging in and out among buildings, using them as cover, as he unloaded useless bursts of fire into the angel's AT Field. Unfortunately, the limited supply of buildings eventually forced Shinji to back out of the vicinity of the city in order to buy himself some time and minimize the damage caused to his surroundings.

"Misato! How long do I have to keep my distance?" shouted Shinji, tired of running away from the angel. Before she could answer though, Misato was horrified to notice two civilians on the hills right in front of the EVA directly in its path.

"Shinji watch out!" yelled Misato.

Shinji saw the two civilians as he was about to take the next step, which would have landed right on top of them, and twisted to avoid them just in time. However, doing so caused him to lose his balance, making the EVA fall hard onto the nearby hills. To make matters worse, the angel used this opportunity to slice off the umbilical cable connected to the EVA, cutting off Shinji from the external power source.

4.59...

Everyone on the bridge jumped out of their chairs simultaneously, instantly going to work on how much time the EVA had left, what the distance to the next external power source was, how far the target was, etc etc, yelling out commands and requests for data. The entire bridge fell into a cacophony of organized chaos. Within moments, a calculated projection of where the best strategic location was to reconnect the EVA, how long it took to get there, and which course the EVA should take in order to minimize the chance of interference by the target was made. The immediate emergency having been taken care of, the bridge crew handed the report into the waiting hands of Captain Katsuragi and sat back in their seats to observe the rest of the battle nervously, ready at any moment to spring back into action.

While this was happening, Shinji zoomed in his screen to find out that the two civilians were none other than his classmates, Kensuke and Toji, the latter of whom had so nicely punched Shinji in the face just a few hours ago.

_IDIOTS!_

Realizing there was no possible way he was going to be able to fight with them out on the surface, Shinji activated the on-board plug release and yelled out at the two boys frozen solid from almost having been crushed by a skyscraper-sized mecha. "Get your asses in here now!"

Ritsuko paled at that. "Shinji! What are you doing?! The EVA is a highly classified weapon! You can't just let civilians inside the plug!" she yelled.

"Sorry Doctor, I don't have a choice." was the only reply Shinji gave as he helped the two boys into the plug.

As soon as they were inside the plug, Shinji re-secured the hatch and synced back with the EVA.

3.24...

"First off. You guys are idiots. Secondly, you can breathe through this liquid so don't hold your breath. And third, shut up and stay still if you want to live." growled Shinji. Kensuke and Toji could do nothing but nod vigorously as they continued to consolidate their terror at what was happening.

"Shinji! You don't have much time! There is a secondary power source in sector 12 of the city, at your fastest it should take about a minute to get there. Get to it!" commanded Misato.

2.52...

Without a word, Shinji started sprinting towards the building, still trying to avoid the angel's onslaught of attacks, which seemed to be even fiercer than before. Struggling to run as fast as he can and avoid the reaching tentacles at the same time, Shinji tripped on the rubble of one of the destroyed buildings and fell forward. The angel, sensing the EVA's temporary vulnerability, struck.

"Shinji watch out!"

But it was too late. Shinji cried out in pain as the angel penetrated the EVA's chest. Watching from behind the cockpit seat, Toji looked at Kensuke with a horrified expression on his face. He had not known that Shinji would be able to feel whatever the EVA felt. Kensuke returned the expression, just as shocked as he was.

"Shinji! Are you alright?" yelled out Misato. "Pull yourself together! It's coming at you again!"

Gritting his teeth, Shinji forced his EVA to get up, ignoring the blinding pain in his chest. As soon as he did so, the angel sent out another thrash of attacks, intent on keeping the Evangelion down. The attack missed Shinji by a wide margin. Shinji got the Evangelion to its feet and abruptly, the pain in his chest vanished. Sighing in relief, Shinji got the EVA back in motion towards the power source only to find that the last attack had not been meant for Shinji at all. It had targeted what Shinji was going for!

"Tower 2 destroyed! No more towers in Unit 01's immediate vicinity!"

"Shinji's sync rate has dropped down to 57.3%. Internal nerve connection has been severed at the precise location of puncture! He's not feeling a thing!"

"Impossible!" exclaimed Ritsuko. "No one can control their own sync ratios! Much less hold partial connection to the EVA!"

"Seems like that's all he's been doing, making the impossible possible." murmured Misato, just as astounded by the update.

0.37...

EVA Unit 01 stood back up, now facing the angel. Looking at the data displayed on his screen, he noticed that he only thirty seconds left. It wasn't enough time to get to the next power source and for all he knew, the angel could destroy that one as well before he got there. Plus he was thoroughly annoyed with all this running. He could hear Misato yelling in the background, ordering him to retreat, to take the nearest elevator back down to the hangar, that it is way too dangerous to risk the only Evangelion Unit functional at this point with a race against time, but he ignored her. Instead, he kept his gaze locked on the angel and said, "Hang tight you guys, this is going to be bumpy." As Kensuke and Toji did as Shinji asked, Shinji took a nearby piece of rubble and heaved it at the angel. The angel responded to this by slicing up the huge piece of rock into pieces, chunks of it flying everywhere. Smiling, Shinji took another, bigger piece of rubble from a nearby pile and heaved it using as much strength as the EVA could muster. As he did so, Shinji charged with the momentum of his throw, trailing right behind the flying boulder.

0.06...

As expected, the angel used its laser charged tentacles to decimate this boulder as well, spraying debris and dust everywhere. And through this, Shinji charged, using all his might to jump straight into where he knew the angel would be standing.

0.03...

The EVA twisted in the air like a drill in order to gain more momentum and force as it shot through the air through the debris. Mid twist, Shinji pulled out his prog knife as it hummed to life...

0.01...

...and he jammed it into the angel's core. It was almost a perfect reenactment of the simulation training that he had done the night before, with bits of improvisation added into it. The angel thrashed wildly, trying to throw the purple behemoth off itself while Shinji twisted the blade.

0.00.

Unit 01's external powered down, and Shinji no longer could see what was happening. He noticed he had been holding his breath and released it. His hands were calloused from having held on to the controls so tightly. But he had done it. He had defeated the angel. Behind him, he heard Kensuke and Toji finally release their breaths as well. "Wow" was all Toji could muster. Kensuke nodded, agreeing with whatever sentiments Toji was feeling.

"I know right?" Shinji said, giving both of them a relieved grin. After a moment, Kensuke returned the grin, and Toji as well, albeit with a little reluctance. The three of them knew, at that moment, staring at each other through LCL after having experienced a near-death situation together, that a bond had formed between them.

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After the medical crew arrived and had examined both Shinji and his two new friends, Misato appeared on the scene. She stalked up to the three of them with a furious expression on her face. Stopping in front of them, she turned her glare on Kensuke and Toji. "You two. Wait right there. I will deal with you in a moment."

Then, her expression suddenly softened as she turned her attention to Shinji. "Are you ok Shinji? That was quite a blow you received." Kensuke and Toji goggled, envying Shinji for the positive attention he was getting from this breath-taking raven-haired beauty. Shinji, on the other hand, was just relieved to find out she wasn't going to kick his ass for ignoring her orders during the battle and replied that he was fine and that the pain had only been momentary. He had judged too soon. As soon as Misato verified that Shinji was not hurt and was, in fact, fine both in body and mind, she slapped him across the face. Hard.

"How dare you ignore my orders to retreat!" yelled Misato. Eyes widening, Kensuke and Toji tried to slip away as Misato unloaded on Shinji about the importance of obeying orders on the field and how he could have endangered the entire city with his recklessness. "You two! I told you to stay where you are!"

Toji and Kensuke froze. So for over 30 minutes, they were forced to stand there and watch sympathetically as Shinji was scolded for his inconsiderate and dangerous actions in the battlefield. Shinji, on the receiving end of this brutality, listened calmly because, well, what else was he going to do?

Then, all of a sudden, Shinji's vision went white as pain such as he had never felt before in his life crashed into his chest. Shinji must have collapsed because he could faintly hear Misato screaming for a medic, that Shinji had collapsed, but it all seemed so far away. His world was nothing but pain; everything else seemed inconsequential beside the agony.

Then, thankfully, blackness claimed him.

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A/N - End of Chapter 3. Sorry if I'm a bit delayed in uploading the next few chapters. March Madness is here! Read and Review please! Oh, and I'm still looking for Beta Readers. :D


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